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aertslab / pySCENIC

pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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[BUG] pySCENIC installation error #531

Open strawberry098 opened 6 months ago

strawberry098 commented 6 months ago

I git clone with development version of pySCENIC. Upon pip3 install ., I get the following error:

Collecting ctxcore>=0.2.0 (from pyscenic==0.12.1+7.g1cd059f) Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:877)'),)': /simple/ctxcore/ Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:877)'),)': /simple/ctxcore/ Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:877)'),)': /simple/ctxcore/ Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:877)'),)': /simple/ctxcore/ Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:877)'),)': /simple/ctxcore/ Could not fetch URL https://pypi.python.org/simple/ctxcore/: There was a problem confirming the ssl certificate: HTTPSConnectionPool(host='pypi.org', port=443): Max retries exceeded with url: /simple/ctxcore/ (Caused by SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:877)'),)) - skipping Could not find a version that satisfies the requirement ctxcore>=0.2.0 (from pyscenic==0.12.1+7.g1cd059f) (from versions: ) No matching distribution found for ctxcore>=0.2.0 (from pyscenic==0.12.1+7.g1cd059f)

ghuls commented 6 months ago

Could you try again? This error is not related to pySCENIC itself, but with pypi.org or your local certificate store. It could be that there was a temporarily certificate problem on pypi's part, or you need to update your local certificate store to have the latest certificates.

On Ubuntu/Debian based distributions: https://www.cyberciti.biz/faq/update-ca-certificates-command-examples-in-linux-to-ssl-ca-certificates/